Crystal structure of 3-methyl­pyridine-2-carbaldehyde 4-methyl­thio­semi­carba­zone monohydrate

Abstract

In the title hydrate, C₉H₁₂N₄S·H₂O (systematic name: 3-methyl-1-{(E)-[(3-methyl­pyridin-2-yl)methyl­idene]amino}­thio­urea monohydrate), a small twist is noted between the pyridine ring and the rest of the organic mol­ecule [dihedral angle = 6.96 (5)°]. The imine and pyridine N atoms are syn, and the amine H atoms are anti. The latter arrangement allows for the formation of an intra­molecular N—H⋯N(imine) hydrogen bond. Both the N-bonded H atoms form hydrogen bonds to symmetry-related water mol­ecules, and the latter forms O—H hydrogen bonds with the pyridine N and thione S atoms. These inter­actions lead to supra­molecular layers that stack along the a-axis direction with no specific inter­actions between them.

Related literature  

For background to the coordination chemistry of thio­semicarbazones, see: Beraldo et al. (2001 ▸); Sreekanth et al. (2004 ▸). For the structure of the parent compound, in which the pyridine N atom is anti to the imine N atom, see: West et al. (1996 ▸). For the synthesis of the title compound, see: Ali et al. (1997 ▸).

Experimental  

Crystal data  

• C₉H₁₂N₄S·H₂O

• M _r = 226.30

• Monoclinic,

• a = 10.4493 (3) Å

• b = 13.6989 (3) Å

• c = 8.0235 (3) Å

• β = 102.816 (3)°

• V = 1119.90 (6) ų

• Z = 4

• Cu Kα radiation

• μ = 2.42 mm⁻¹

• T = 100 K

• 0.30 × 0.20 × 0.10 mm

Data collection  

• Oxford Diffraction Xcaliber Eos Gemini diffractometer

• Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011 ▸) T _min = 0.860, T _max = 1.000

• 14591 measured reflections

• 2160 independent reflections

• 2044 reflections with I > 2σ(I)

• R _int = 0.022

Refinement  

• R[F ² > 2σ(F ²)] = 0.034

• wR(F ²) = 0.097

• S = 1.05

• 2160 reflections

• 150 parameters

• 5 restraints

• H atoms treated by a mixture of independent and constrained refinement

• Δρ_max = 0.31 e Å⁻³

• Δρ_min = −0.25 e Å⁻³

Data collection: CrysAlis PRO (Agilent, 2011 ▸); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2015 ▸); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015 ▸); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012 ▸) and DIAMOND (Brandenburg, 2006 ▸); software used to prepare material for publication: publCIF (Westrip, 2010 ▸).

Supplementary Material

CCDC reference: 1053448

Additional supporting information: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (, ).

DHA	DH	HA	D A	DHA
N4H4NN2	0.88(2)	2.19(2)	2.6116(16)	109(1)
N1H1NO1W i	0.88(1)	2.12(1)	2.9940(15)	170(2)
N4H4NO1W	0.88(2)	2.50(2)	3.3100(15)	154(1)
O1WH1WN3	0.84(2)	2.11(2)	2.9371(16)	172(2)
O1WH2WS1ii	0.85(2)	2.50(2)	3.3412(11)	173(2)

Symmetry codes: (i) ; (ii) .

supplementary crystallographic information

S2. Experimental

The Schiff base ligand was prepared according to Ali et al. (1997). 4-Methyl-3-thiosemicarbazide (0.01 mol) was dissolved in hot 95% ethanol (50 ml), and an equimolar amount of 3-methylpyridine-2-carbaldehyde in the same solvent (20 ml) was added. The mixture was heated with occasional stirring until the volume reduced to 20 ml. It was allowed to stand overnight and a yellow precipitate formed, which was filtered off and washed with cold ethanol. Crystals suitable for X-ray diffraction analysis were obtained by recrystallization from ethanol. Yields were high, ca. 92%.

S3. Refinement

Carbon-bound H-atoms were placed in calculated positions (C—H = 0.95 to 0.98 Å) and were included in the refinement in the riding model approximation with U_iso(H) = 1.2–1.5U_eq(C). The O—H atoms were refined with O—H = 0.84±0.01 Å, and with U_iso(H) = 1.5U_eq(O). The N—H H atoms were treated similarly with N—H = 0.88±0.01 Å and U_iso(H) = 1.2U_eq(N).

Figures

Fig. 1.

The molecular structure of the title compound showing the atom-labelling scheme and displacement ellipsoids at the 70% probability level.

Fig. 2.

A view of the supramolecular layer in parallel to (1 0 0) sustained by N—H···O (blue dashed lines), O—H···N (pink) and O—H···S (orange) hydrogen bonding.

Fig. 3.

A view of the unit-cell contents in projection down the c axis. The N—H···O (blue), O—H···N (pink) and O—H···S (orange) hydrogen bonds are shown as dashed lines.

Crystal data

C9H12N4S·H2O	F(000) = 480
Mr = 226.30	Dx = 1.342 Mg m−3
Monoclinic, P21/c	Cu Kα radiation, λ = 1.5418 Å
a = 10.4493 (3) Å	Cell parameters from 7855 reflections
b = 13.6989 (3) Å	θ = 3.2–71.2°
c = 8.0235 (3) Å	µ = 2.42 mm−1
β = 102.816 (3)°	T = 100 K
V = 1119.90 (6) Å3	Prism, pale-brown
Z = 4	0.30 × 0.20 × 0.10 mm

Data collection

Oxford Diffraction Xcaliber Eos Gemini diffractometer	2160 independent reflections
Radiation source: fine-focus sealed tube	2044 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.022
Detector resolution: 16.1952 pixels mm-1	θmax = 71.4°, θmin = 4.3°
ω scans	h = −12→12
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011)	k = −16→16
Tmin = 0.860, Tmax = 1.000	l = −9→9
14591 measured reflections

Refinement

Refinement on F2	5 restraints
Least-squares matrix: full	Hydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.034	H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.097	w = 1/[σ2(Fo2) + (0.0657P)2 + 0.3425P] where P = (Fo2 + 2Fc2)/3
S = 1.05	(Δ/σ)max = 0.001
2160 reflections	Δρmax = 0.31 e Å−3
150 parameters	Δρmin = −0.25 e Å−3

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
S1	0.73687 (3)	0.84153 (2)	0.49693 (4)	0.01984 (14)
N1	0.52525 (11)	0.80894 (8)	0.61677 (14)	0.0178 (3)
H1N	0.5225 (16)	0.8721 (7)	0.636 (2)	0.021*
N2	0.43392 (11)	0.74878 (8)	0.66067 (14)	0.0178 (3)
N3	0.25907 (11)	0.63228 (8)	0.77276 (14)	0.0199 (3)
N4	0.62430 (11)	0.67137 (8)	0.54238 (14)	0.0187 (3)
H4N	0.5662 (14)	0.6409 (12)	0.588 (2)	0.022*
C1	0.62415 (13)	0.76805 (9)	0.55465 (16)	0.0168 (3)
C2	0.34637 (13)	0.78964 (9)	0.72608 (16)	0.0177 (3)
H2	0.3482	0.8582	0.7437	0.021*
C3	0.24297 (13)	0.73011 (10)	0.77382 (16)	0.0168 (3)
C4	0.16527 (14)	0.57657 (10)	0.81199 (18)	0.0228 (3)
H4	0.1760	0.5077	0.8116	0.027*
C5	0.05263 (14)	0.61413 (10)	0.85338 (18)	0.0224 (3)
H5	−0.0125	0.5719	0.8792	0.027*
C6	0.03765 (13)	0.71450 (10)	0.85609 (17)	0.0211 (3)
H6	−0.0381	0.7420	0.8848	0.025*
C7	0.13356 (13)	0.77500 (9)	0.81675 (16)	0.0177 (3)
C7'	0.11857 (15)	0.88417 (10)	0.8229 (2)	0.0270 (3)
H7'1	0.0318	0.9001	0.8432	0.040*
H7'2	0.1274	0.9125	0.7139	0.040*
H7'3	0.1867	0.9109	0.9158	0.040*
C8	0.72818 (13)	0.61612 (11)	0.49226 (17)	0.0225 (3)
H8A	0.7460	0.6438	0.3871	0.034*
H8B	0.7008	0.5479	0.4724	0.034*
H8C	0.8079	0.6194	0.5834	0.034*
O1W	0.49697 (10)	0.51694 (7)	0.77859 (13)	0.0232 (2)
H1W	0.4330 (14)	0.5544 (12)	0.774 (2)	0.035*
H2W	0.5595 (14)	0.5483 (13)	0.841 (2)	0.035*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
S1	0.0178 (2)	0.0182 (2)	0.0254 (2)	−0.00111 (11)	0.00872 (14)	−0.00060 (11)
N1	0.0179 (6)	0.0137 (5)	0.0231 (6)	−0.0011 (4)	0.0075 (5)	−0.0007 (4)
N2	0.0173 (6)	0.0177 (5)	0.0179 (6)	−0.0021 (4)	0.0030 (4)	0.0011 (4)
N3	0.0194 (6)	0.0163 (5)	0.0238 (6)	0.0013 (4)	0.0045 (5)	0.0013 (4)
N4	0.0197 (6)	0.0163 (6)	0.0210 (6)	0.0006 (4)	0.0060 (5)	0.0001 (4)
C1	0.0163 (6)	0.0182 (6)	0.0152 (6)	0.0009 (5)	0.0017 (5)	0.0002 (5)
C2	0.0181 (6)	0.0146 (6)	0.0197 (6)	−0.0005 (5)	0.0029 (5)	0.0006 (5)
C3	0.0164 (6)	0.0175 (6)	0.0154 (6)	0.0000 (5)	0.0015 (5)	0.0005 (5)
C4	0.0244 (7)	0.0159 (6)	0.0282 (7)	−0.0005 (5)	0.0061 (6)	0.0023 (5)
C5	0.0208 (7)	0.0205 (7)	0.0266 (7)	−0.0044 (5)	0.0066 (5)	0.0025 (5)
C6	0.0174 (6)	0.0238 (7)	0.0226 (7)	0.0010 (5)	0.0055 (5)	−0.0003 (5)
C7	0.0184 (6)	0.0168 (7)	0.0172 (6)	0.0002 (5)	0.0024 (5)	0.0002 (5)
C7'	0.0292 (8)	0.0172 (7)	0.0385 (8)	0.0030 (6)	0.0161 (6)	−0.0008 (6)
C8	0.0217 (7)	0.0187 (7)	0.0261 (7)	0.0051 (5)	0.0036 (6)	−0.0024 (5)
O1W	0.0207 (5)	0.0180 (5)	0.0309 (5)	0.0003 (4)	0.0055 (4)	−0.0032 (4)

Geometric parameters (Å, º)

S1—C1	1.6903 (13)	C4—H4	0.9500
N1—C1	1.3633 (17)	C5—C6	1.385 (2)
N1—N2	1.3649 (15)	C5—H5	0.9500
N1—H1N	0.881 (9)	C6—C7	1.3896 (19)
N2—C2	1.2801 (18)	C6—H6	0.9500
N3—C4	1.3338 (18)	C7—C7'	1.5057 (18)
N3—C3	1.3510 (17)	C7'—H7'1	0.9800
N4—C1	1.3281 (17)	C7'—H7'2	0.9800
N4—C8	1.4513 (17)	C7'—H7'3	0.9800
N4—H4N	0.879 (9)	C8—H8A	0.9800
C2—C3	1.4706 (18)	C8—H8B	0.9800
C2—H2	0.9500	C8—H8C	0.9800
C3—C7	1.4066 (18)	O1W—H1W	0.836 (9)
C4—C5	1.391 (2)	O1W—H2W	0.848 (9)
C1—N1—N2	118.45 (11)	C6—C5—H5	120.8
C1—N1—H1N	121.7 (11)	C4—C5—H5	120.8
N2—N1—H1N	119.6 (11)	C5—C6—C7	119.93 (13)
C2—N2—N1	116.49 (11)	C5—C6—H6	120.0
C4—N3—C3	117.84 (12)	C7—C6—H6	120.0
C1—N4—C8	123.63 (12)	C6—C7—C3	117.47 (12)
C1—N4—H4N	115.5 (12)	C6—C7—C7'	119.96 (12)
C8—N4—H4N	119.7 (11)	C3—C7—C7'	122.58 (12)
N4—C1—N1	116.76 (12)	C7—C7'—H7'1	109.5
N4—C1—S1	124.14 (10)	C7—C7'—H7'2	109.5
N1—C1—S1	119.10 (10)	H7'1—C7'—H7'2	109.5
N2—C2—C3	119.83 (12)	C7—C7'—H7'3	109.5
N2—C2—H2	120.1	H7'1—C7'—H7'3	109.5
C3—C2—H2	120.1	H7'2—C7'—H7'3	109.5
N3—C3—C7	122.98 (12)	N4—C8—H8A	109.5
N3—C3—C2	116.66 (12)	N4—C8—H8B	109.5
C7—C3—C2	120.36 (12)	H8A—C8—H8B	109.5
N3—C4—C5	123.36 (13)	N4—C8—H8C	109.5
N3—C4—H4	118.3	H8A—C8—H8C	109.5
C5—C4—H4	118.3	H8B—C8—H8C	109.5
C6—C5—C4	118.41 (12)	H1W—O1W—H2W	102.7 (18)
C1—N1—N2—C2	176.76 (11)	C3—N3—C4—C5	0.1 (2)
C8—N4—C1—N1	−174.76 (11)	N3—C4—C5—C6	−0.8 (2)
C8—N4—C1—S1	5.79 (18)	C4—C5—C6—C7	0.5 (2)
N2—N1—C1—N4	−0.36 (17)	C5—C6—C7—C3	0.53 (19)
N2—N1—C1—S1	179.12 (9)	C5—C6—C7—C7'	−178.83 (12)
N1—N2—C2—C3	178.85 (11)	N3—C3—C7—C6	−1.32 (19)
C4—N3—C3—C7	1.02 (19)	C2—C3—C7—C6	178.27 (12)
C4—N3—C3—C2	−178.58 (11)	N3—C3—C7—C7'	178.02 (12)
N2—C2—C3—N3	11.03 (18)	C2—C3—C7—C7'	−2.39 (19)
N2—C2—C3—C7	−168.58 (12)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N4—H4N···N2	0.88 (2)	2.19 (2)	2.6116 (16)	109 (1)
N1—H1N···O1Wi	0.88 (1)	2.12 (1)	2.9940 (15)	170 (2)
N4—H4N···O1W	0.88 (2)	2.50 (2)	3.3100 (15)	154 (1)
O1W—H1W···N3	0.84 (2)	2.11 (2)	2.9371 (16)	172 (2)
O1W—H2W···S1ii	0.85 (2)	2.50 (2)	3.3412 (11)	173 (2)

Symmetry codes: (i) −x+1, y+1/2, −z+3/2; (ii) x, −y+3/2, z+1/2.